@article{sukno_mccuiston_wong_wang_thon_hussey_baum_davis_2007, title={Quantitative detection of double-stranded RNA-mediated gene silencing of parasitism genes in Heterodera glycines}, volume={39}, number={2}, journal={Journal of Nematology}, author={Sukno, S. A. and McCuiston, J. and Wong, M. Y. and Wang, X. H. and Thon, M. R. and Hussey, R. and Baum, T. and Davis, E.}, year={2007}, pages={145–152} }
 @article{kulkarni_thon_pan_dean_2005, title={Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea}, volume={6}, number={3}, journal={Genome Biology}, author={Kulkarni, R. D. and Thon, M. R. and Pan, H. Q. and Dean, R. A.}, year={2005} }
 @article{thon_martin_goff_wing_dean_2004, title={BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea}, volume={41}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2004.02.003}, abstractNote={Transposable elements (TEs) are viewed as major contributors to the evolution of fungal genomes. Genomic resources such as BAC libraries are an underutilized resource for studying genome-wide TE distribution. Using the BAC end sequences and physical map that are available for the rice blast fungus, Magnaporthe grisea, we describe a likelihood ratio test designed to identify clustering of TEs in the genome. A significant variation in the distribution of three TEs, MAGGY, MGL, and Pot2 was observed among the fingerprint contigs of the physical map. We utilized a draft sequence of M. grisea chromosome 7 to validate our results and found a similar pattern of clustering. By examining individual BAC end sequences, we found evidence for 11 unique integrations of MAGGY or MGL into Pot2 but no evidence for the reciprocal integration of Pot2 into another TE. This suggests that: (a) the presence of Pot2 in the genome predates that of the other TEs, (b) Pot2 was less transpositionally active than other TEs, or (c) that MAGGY and MGL have integration site preference for Pot2. High transition/transversion mutation ratios as well as bias in transition site context was observed in MAGGY and MGL elements, but not in Pot2 elements. These features are consistent with the effects of a Repeat-Induced Point (RIP) mutation-like process occurring in MAGGY and MGL elements. This study illustrates the general utility of a physical map and BAC end sequences for the study of genome-wide repetitive DNA content and organization. Index Descriptors: Transposon; Transposable element; Rice blast; Magnaporthe grisea; Pyricularia grisea; BAC library; Physical map}, number={7}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Thon, MR and Martin, SL and Goff, S and Wing, RA and Dean, RA}, year={2004}, month={Jul}, pages={657–666} }
 @article{ebbole_jin_thon_pan_bhattarai_thomas_dean_2004, title={Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: Analysis of expressed sequence tags}, volume={17}, ISSN={["0894-0282"]}, DOI={10.1094/MPMI.2004.17.12.1337}, abstractNote={ Over 28,000 expressed sequence tags (ESTs) were produced from cDNA libraries representing a variety of growth conditions and cell types. Several Magnaporthe grisea strains were used to produce the libraries, including a nonpathogenic strain bearing a mutation in the PMK1 mitogen-activated protein kinase. Approximately 23,000 of the ESTs could be clustered into 3,050 contigs, leaving 5,127 singleton sequences. The estimate of 8,177 unique sequences indicates that over half of the genes of the fungus are represented in the ESTs. Analysis of EST frequency reveals growth and cell type-specific patterns of gene expression. This analysis establishes criteria for identification of fungal genes involved in pathogenesis. A large fraction of the genes represented by ESTs have no known function or described homologs. Manual annotation of the most abundant cDNAs with no known homologs allowed us to identify a family of metallothionein proteins present in M. grisea, Neurospora crassa, and Fusarium graminearum. In addition, multiply represented ESTs permitted the identification of alternatively spliced mRNA species. Alternative splicing was rare, and in most cases, the alternate mRNA forms were unspliced, although alternative 5′ splice sites were also observed. }, number={12}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Ebbole, DJ and Jin, Y and Thon, M and Pan, HQ and Bhattarai, E and Thomas, T and Dean, R}, year={2004}, month={Dec}, pages={1337–1347} }